[FLIMfit-users] Exporting FLIMfit data and boundaries for beta values

[Munro, Ian]

Hello again Emilie

Just to clarify a couple of points now that I’m back at work.
Firstly, in addition to being able to control the colour map range , as I described earlier, FLIMfit also allows you to invert the colour map used.

If  this doesnn’t give you exactly the display you need then as Sean describes you can simply export the fitted data as a .tiff and re-import into Matlab to display as you wish using File-> Export Images.
However please be aware  that the exported .tiff contains NaNs in those pixels which were excluded from the fit using the “Integrated Min” Intensity threshold on the Data tab.
You may, therefore, have to replace these with a suitable value in order to get the display that you require.

Best Regards

Ian



On 27 Dec 2015, at 12:23, Warren, Sean Christopher <sean.warren09 at imperial.ac.uk<mailto:sean.warren09 at imperial.ac.uk>> wrote:

Dear Emilie,

Apologies for the delay replying, I'm glad you're finding FLIMfit useful!
Hopefully the following should help:

>Is it possible to export FLIMfit results to matlab, such that I can make changes to the colours and not have the lifetime range written in the image itself.
Yes, the raw lifetime (or other parameter values) may be exported as floating point TIFF files using the following procedure:

  *   In the images tab, select the desired parameters for export from the list on the right. Use the first tick box, not the second which displays the intensity merged images.
  *   From the menu, select File>Export Selected Images... and choose a root filename
  *   For all the processed images, all of the selected parameters will be exported as images. There will be one colour mapped image with the lifetime scale and one with 'raw' in the filename which contains the true lifetime values and may be opened in MATLAB etc.


> Is it possible to display the IRF shift?
The IRF shift is displayed as 't0' (for time zero) in the parameter tab and images when fitted.


> Would it be possible to fix the beta values between certain values, for instance always positive?
For technical reasons, this is not currently possible using global analysis. However, if you set the fitting algorithm to 'Maximum Likelihood' in the Advanced fitting tab the beta values will be constrained to positive values. This will only work for 'pixelwise' fitting (i.e. fitting pixels independently).

It's worth noting that if you're consistently observing negative beta values this is often due to a mismatch between the model and the data which is being compensated by fitting negative values. Examples of potential problems include a difference in the IRF shift between the measured IRF (or reference) and the data, an uncompensated background component, or, in the case of FRET, a donor with a complex decay. If you'd like to discuss this further please feel free to drop me an email.


Best Regards,
Sean

________________________________
From: FLIMfit-users [flimfit-users-bounces at lists.openmicroscopy.org.uk<mailto:flimfit-users-bounces at lists.openmicroscopy.org.uk>] on behalf of Munro, Ian [i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>]
Sent: Wednesday, 23 December 2015 07:46
To: Wientjes, Emilie; 'flimfit-users at lists.openmicroscopy.org.uk<mailto:flimfit-users at lists.openmicroscopy.org.uk>'
Subject: Re: [FLIMfit-users] Exporting FLIMfit data and boundaries for beta values


Hi Emile

Glad to hear you're finding FLIMfit useful. I'm afraid I'm away from the office now until next year and only have a phone with me so can't reply in full but p!ease note that you can manually set the range over which the colour map is stretched by unticking the 'auto' box at top right  in the images tab . I hope this helps for now.


Kind regards

Ian
________________________________
From: FLIMfit-users <flimfit-users-bounces at lists.openmicroscopy.org.uk<mailto:flimfit-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Wientjes, Emilie <emilie.wientjes at wur.nl<mailto:emilie.wientjes at wur.nl>>
Sent: 18 December 2015 10:56:09
To: 'flimfit-users at lists.openmicroscopy.org.uk<mailto:flimfit-users at lists.openmicroscopy.org.uk>'
Subject: [FLIMfit-users] Exporting FLIMfit data and boundaries for beta values

Dear All,

I am a new FLIMfit user and I like it :)

However, I have few extra wishes/questions:
-      Is it possible to export FLIMfit results to matlab, such that I can make changes to the colours and not have the lifetime range written in the image itself?
-      Is it possible to display the IRF shift?
-      Would it be possible to fix the beta values between certain values, for instance always positive?

Thanks,
Kind regards,

Emilie Wientjes
Laboratory of Biophysics

Dreijenlaan 3
6703 HA Wageningen
The Netherlands
Tel: +31317485129





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